No vehicle is completely free from noise and some are worse than others. The noise is generally created by a vibrating panel or by two pieces of the vehicle making intermittent contact. The vibration can be caused by the bass generated by the stereo or simply by driving a less than perfect vehicle on a less than perfect road. This page will help you to identify the cause and will help you eliminate it to a point where it's no longer a problem.

Resonance:
The resonant frequency is the frequency at which a piece of metal, plastic or anything else swings/vibrates with the least amount of energy input. Think of a person on a playground swing. You know that it takes very little effort to keep the person swinging. The frequency at which they swing back and forth is their resonant frequency. If you try to make them swing faster or slower, it will take significantly more energy.

Resonating Panels:
This type of noise is caused when the bass notes are the same frequency as the resonant frequency of a metal or plastic panel. To stop or reduce the noise associated with this type of problem, you can do a couple of things.

If the panel is close to another panel or brace, you can connect the panel to the brace with some sort of filler. If the trunk lid is resonating, you could put some sort of foam weather stripping material in-between the brace and the trunk lid. You could also use silicone to fill the gap between the 2 pieces. This will stop the trunk lid from resonating. Some people use expanding foam, and it may work but you MUST be sure to fill the gap very slowly. If the expanding foam is not able to spread out quickly enough, the two pieces may be forcibly pushed apart. My suggestion would be to use a closed cell weather stripping type of material. You will immediately know if you fixed the problem without having to wait for anything to dry or cure.

If the trunk lid (or any other resonating panel) is not near a brace, you may have to add mass to the panel. This is usually done with some sort of damping material. The damping material may have an adhesive backing or could be the type that is sprayed/brushed on. You will have to add enough mass to lower the resonant frequency to below the bass frequencies. If the resonant frequency can't be lowered to below the lowest bass notes, the added damping material may make the panel massive enough so that the bass doesn't have enough energy to significantly vibrate the panel. THIS is a link to a page from the McMaster-Carr site. The bottom of the page shows several different damping materials that can be used for damping the vibrations of resonating panels.

Rattling:
This type of noise would be caused when 2 pieces of metal, plastic, whatever... are close enough to slam into each other when they resonate. This is probably best solved by filling the gap between the two vibrating parts with silicone sealant or closed cell foam weather stripping. The weather stripping is a better solution in places like behind the license plate. If you have a license plate frame, you can get some really thin weather stripping and put between the frame and the plate.